Optimize parametersWhen you perform peptide mass fingerprinting (PMF) you usually start out with a protein separation on gels, perform in-gel digest, extract the peptides, analyse by mass spectrometry, extract the peptide mass list and finally use this list to search a database using a program like Mascot, ProFound or similar.

In many cases you just want to identify the protein, and if the score is significant enough you are done. However, in other cases your identification is borderline.In other cases you want to verify as much of the protein as possible (i.e. generate a high sequence coverage).